


Missing

by Kindred



Category: Guardians of the Galaxy (Movies), Iron Man (Movies), Spider-Man (Tom Holland Movies), The Avengers (Marvel Movies)
Genre: Dead May Parker (Spider-Man), Emotional Hurt/Comfort, Hurt Peter Parker, Hurt/Comfort, Implied/Referenced Rape/Non-con, M/M, Mpreg, Non-Traditional Alpha/Beta/Omega Dynamics, Peter Parker is a Mess, Peter Quill Feels, Precious Peter Parker, Protective Peter Quill, Protective Tony Stark, Quentin Beck Being a Jerk, Running Away, Tony Stark Acting as Peter Parker's Parental Figure, Tony Stark Has A Heart, Tony Stark is alive, Villain Quentin Beck
Language: English
Status: Completed
Published: 2020-02-02
Updated: 2020-03-14
Packaged: 2021-03-12 15:40:48
Rating: Mature
Warnings: Rape/Non-Con, Underage
Chapters: 5
Words: 4,382
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/22525861
Author URL: https://archiveofourown.org/users/Kindred/pseuds/Kindred
Summary: “What’s up Earthling?”“Oi Flash Gordon it’s Tony Stark!”
Relationships: Pepper Potts/Tony Stark, Peter Parker & Tony Stark, Peter Parker/Peter Quill, Quentin Beck/Peter Parker
Comments: 30
Kudos: 88





	1. Chapter 1

Tony Stark felt like he was slammed back to life, one moment he was dead thinking of nothing feeling nothing and then everything hurt and that was all he could think about was the pain in his body. Until he heard someone call his name “Tony can you hear me?” Came the soft voice, he groaned his mouth felt was dryer than desert and his brain was rattling he could swear he felt it moving. “Tony?”  
“I thought I was dead?” He mumbled,   
“You were.” Came the sob mixed with laughter   
“Then who woke me up?” He still hasn’t opened his eyes as he let his hand tangle with Pepper’s hair as she rests her head on his chest. “You’ve had a hair cut?” He mumbled “Is it a cute pixie look? Or sexy edgey look?” He asked as he felt her shoulder shake. 

He felt Pepper kiss his hand and that forced him to open his eyes and look at her, the light in the room was too bright and made him hiss and close his eyes “Friday lower the lights.” Pepper asked, “We don’t know how you came back Tony, It was Stephen who found you.” Tony frowned and looked up at her.   
“Stephen?”  
“Doctor Strange.” She tells him, he raises an eyebrow at him and this got her to smile at the look as she tried not to cry.  
“First name base? Should I be worried?” He asked, she chuckled and shook her head kissing his hand again as she cupped her faces making her nuzzle his hand.  
“No, he has been helping me find...” She stopped her eyes looked wide for a moment and Tony saw a flash of guilt, fear and then sadness cross her eyes. Pepper looked down at the bed unsure if she should tell him, Tony frowned as he watches her.  
“What is it?” He asked “What happen? Morgan is she okay?” He asked looking fearful  
“She fine Tony.” He let out a sigh of relief and leans back in his bed,   
“Harley?”   
“He is doing great too.” She knew where this was going but it still caught in her throat to think of what she was going to tell Tony.   
“Peter? I’m shocked he isn’t here?” He asked that is when Pepper pulled away from him and sat there looking down into her hands. “Pepper? Where is Peter?” He asked, pushing himself up seeing the look on her face. “Pepper?”

The story came out and Pepper wipe the tears off her face as she hands him the tablet “He used to work for you, I checked a brilliant young man but troubled, Beck spent years planning his revenge to get back at you but then the snap happens and he disappeared like everyone else and then when the snap was undone he set his eyes on Peter.” She tells him “He used him more ways than one, Peter did stop him but Beck was set out to destroy Peter not just emotionally or every which way possible.” Tony was quiet as he looked at the articles about Peter being Spiderman. “Jameson was hooked on the idea that Spiderman was bad and that Peter was evil, it escalated even when we did damage control we manage to prove that Beck was behind the attacks and we have proof of what he did to Peter and that helped but Spiderman’s image was tainted.” Tony looked at her with wide eyes.   
“Tell me we dragged this Jameson guy thought the mud?”  
“We brought the Paper he worked for and fired him, he can’t work for another paper or anything that involves reporting news, and he couldn’t even get a job reporting fake news.” Tony could tell she enjoyed it but he still couldn’t help but feel a ‘but’ coming.   
“And Peter?” She let out a small sob.   
“Someone attacked him and his Aunt; he shot Peter and the bullet went through him and into his May.”  
“Aunt May? Is she okay? Is Peter okay?” He asked as he gripped Pepper’s hand, she shook her head before looking at him.   
“May is dead the bullet went through her heart.” Tony just stared at her his mouth no longer working for him “P-Peter left the compound and we haven’t seen him since. That is why Stephen, Doctor Strange has been helping me for the last 3 years to look for him.” 

Meanwhile...  
They have been on Xandar for about a week, Quill needed to do repairs on the ship before they could head off again. The others were off doing whatever it is they do on their weeks off leaving Quill alone with his mate. There was a noise behind him making him pushing himself up from the hole and walked over to the cockpit and pressed the flashing button. “Quill here?”   
“Quill message from your friends from Terra.” Frowning Quill sighed, he figured it will Pepper again to ask him if he has seen Peter. He scratches his head and coughs slightly.  
“Yeah put it through.” He mumbled, “What’s up Earthling?”   
“Oi Flash Gordon it’s Tony Stark!”


	2. Chapter 2

Quill walked into his sleeping quarters, there he stood and watches his sleeping mate curled up under the blankets his back away from him as he slept. Walking closer to the sleeping figure Quill wondered what he going to tell him, there was a whimper and a groan as Peter rolled onto his other side his rest on the small swell of his stomach. Opening his eyes Peter stars at Quill and smiles at him “Hi.”   
“Morning sleeping beauty.” There was a moment of nothing as the omega stared at his Alpha before he moved to stretched letting his back click and then he let out a happy sigh.   
“What have you done?” Peter asked as he sits up and looks at him as he runs his fingers through his hair as he leaned against the head bored  
“I haven’t done anything?” Quill said as he sits on the bed seeing his mate looked up at him with a dull stare.   
“Either you have done something stupid or you are going to do something stupid soooo...?” 

Quill sighed as he hung his head as he scratched his head before turning to look back at Peter who now has a worried look on his face. “What?” He asked as he got up onto his knees letting the sheets fall to his knees as he cupped the man’s face. The alpha looked up at him as he reaches out and touches his bump and sighs.   
“I had a call from Earth again.” Peter stills as he looks down at his mate “Not the normal have you seen Peter call this is different.” The young man frown only deepens as he looks into Quill’s face.   
“W-What do they want?” He asked   
“Tony Stark is alive and he wants me back on Earth, I don’t think he knows but...”  
“He’s alive?” Peter chokes, Quill nods seeing the teen’s eyes start to well up, and he moves and pulls Peter into his arms and got him to sit in his lap. “H-How?” Peter asked,   
“I don’t know, he didn’t say.” He whispered it hurt Quill to see his mate go back to the state he was in when he found him hidden on his ship.

....Flashback...  
Quill had just left Earth and was going to rejoin his friends at Xandar, he had set his course and decide to hide some Earth sweets from the rest of the crew. He walked into his cabin and jumped out of his skin when Peter jumped down on the rood “FUCK KID!” He snapped “What the hell?” Quill yelled as Peter stood there and looked at him his eyes red and puffy he was still in a hospital gown.   
“I-I’m sorry but I didn’t know what else to do, I need to get away from...” Tears were rolling down his cheeks. 

Groaning at the sad omega Quill pulled him in for a hug and let him sob onto his shoulder; Peter latched onto him and cried his whole body shaking. He hated to see omega’s cry normally it was something he’s done to make them cry but this time he knew. He was at the compound when Peter was brought in after he was shot; he knew all about what happen how this Beck man seduces and wormed his way into Peter’s pants then destroyed his life. So he could understand why Peter would run away but he also knew he would have to take him back. But he decides maybe a trap out among the stars wouldn’t hurt the boy. “Listen pup let me get you some clothes yeah; I think I might something that will fight you.” He tells him softly as he cups his face wiping away the tears.   
“Y-You’re not going to see me back?”  
“Naaa I think you need a break, just let me call Boss lady...”  
“No!” Peter yells stopping the alpha “No please I-I just want to disappear please.” He begs, Quill groans again and nods as he gazed into his pleading eyes.   
“Alright fine.”   
....End of Flashback...

He waits for his mate to say something and after a while, Peter pulled himself back and looked at him, he hasn’t seen that hopeless look in a while “We can’t put this off forever.” Quill whispers seeing the sad look in his eyes “I know you’re scared after everything that happens but if we don’t return he would only send someone out to find us.” Peter nodded, it sounds like something Tony would do. He wasn’t sure how he felt at this point.   
“Okay we will go back, b-but I want to speak to Mr Stark first, just so I can be sure it is him.” He sat quietly, Quill nodded he then leans forward and cups his face and kisses on the lips.   
“This will change nothing you’re still my mate.” He tells him softly “He can’t keep us apart.” He smiled as he kisses his shoulder.


	3. Chapter 3

Peter’s morning sickness was worst today, Quill was worried this isn’t the stressed his mate need but what could he do if he didn’t go back he knows Tony would only send someone to find them. He told the other Guardians to take another couple of weeks off as he goes and meets the in-laws. Peter joined him in the cockpit and sits in co-pilot’s seat he sees that his mate is wearing one of his shirt shirts, it was a little big for him and but Quill loves it when Peter is wearing his things. “It will be okay,” Quill whispered as he reaches out and places a hand on Peter’s swollen stomach.

He looked up at alpha and smiled weakly as he placed his hand on top of his and closed his eyes “I-I just don’t know if I can face him, after what I did...”  
“You did nothing wrong, Peter, it’s that bastard and if he wasn’t dead I would have gladly have killed him for he did to you,” Quill growled, Peter shivered always did when Quill growled and it turned him on even when it shouldn’t. A hand cupped his cheek making Peter look up his eyes wide and shining with tears.  
“How long before we arrive?” He asked the alpha’s lips flick at the corners as he leaned down and nuzzled his mate’s throat growling softly at his scent.   
“Oh, we have time if you want a distraction.” Peter dislodged the alpha making Quill frown as he watched him walk away from him and towards the table, they normally have breakfast at. Peter looked over his shoulder as he undid his trousers letting them shimmy down his thighs to his ankles before the omega kicked them off.

Quill licked his lips as he stood up and turned towards Peter as he pulled his shirt off his head and dropped it into his pilot’s seat. He looks at his mate who was now just stood there in Quill’s shirt biting his bottom lip “Are you going to leave me waiting?” Peter asked as he pushed himself up onto the table and spread his legs apart.  
“Not at all darling got to let those Earthlings know who you belong to.” Quill hands slide over the belt and down went the zip and out came the cock. It was already hard and standing to attention begging to be touched, Peter licked his lips as he felt the alpha’s hand skim over his thighs making him shudder as he closes his eyes as he felt the alpha stand between his legs. Peter leans back and pressed his hand onto the bump, Quill growled at the sight as he moved his hand under the shirt over the bump and watched Peter moaned.   
“Don’t tease me.”   
“Not teasing enjoying the view.” He purred as he removed one of his hands and gripped his cock and then guided it to the omega’s slicked dripping hole. He moves forward and slides in Peter threw his head back and moaned as he felt the alpha sink in, his body twitch filled him. Quill started to slowly move as he kept one hand on Peter’s bump “God I love you.” 

Peter moaned as he let his alpha fuck him on what is known as the breakfast table, he moves his hand and wrap them around Quill's neck and kisses him as the alpha’s hands to move to his hips “Mark me again.” Peter moaned as he felt Quill nuzzle his throat, since becoming pregnant Peter liked to be marked over and over again. Quill does worry that one day it will leave a big nasty ugly scar that Peter will hate, but he will not disobey his omega not while he needs him. Quill bite down on the mating scar causing Peter to scream and he cum’s over their stomachs, the alpha moans as he feels his mate tighten around his cock “P-Please.” He hears the whimpers as Peter shakes through his orgasm.

He cums and cums in Peter his hips working overtime to push it in deeper until he collapses on top of his mate. “Oh fuck,” Quill mumbles as he laps at the blood on Peter’s throat, the omega hummed happily to be blessed out as he plays with the alpha’s hair. “I think you have a vampire kink,” Quill mutters, a smile appears on the doe eyes omega’s face as he felt the slight twitch of the alpha’s hips move his cock again.   
“Well, Angel was very sexy.” He sighed; Quill moved and looked down at him with a raised eyebrow.  
“Angel?”  
“We should watch Buffy sometime and then Angel,” Peter tells him as he lets Quill move them to the floor so the alpha didn’t have to support his own weight. He breathes a sigh of relief to know this Angel guy is just a TV vampire and not a real one he really didn’t want to know if he could win against a vampire.

Meanwhile back on Earth...  
Tony was pacing he was pissed at Quill for lying all these years about Peter, the man had his pup with him this whole time and lied. He promised Peter not to kill him but that doesn’t mean he can’t rip him a new one when he gets hands on him. Pepper watched her husband pace even their little girl was copying him pacing up and down with a deep frown on her face. She wanted to laugh at that scene alone but all she could do was cry because this was something she never thought she would see again but at the same time the stress of finding out that space Monkey has been lying to her all this time made her want to break down.

He stopped and looked at Pepper before walking over to her and cupping her face the Beta smiled tiredly at him “I’m sorry I should have...”  
“This isn’t your fault, Quill could have told you at any time that he has Peter with him and that done cocky sod didn’t. I know Peter had his own reason for not saying anything but damn it he could have just said hi once in a while.” Tony mumbled as he ran his fingers through his hair, he understood Peter’s thought run until it stopped hurting the problem was he left it so long that it becomes painful just to talk to those that are still there for him.


	4. Chapter 4

The closer they got the worst Peter felt, even with Quill and his amazing dick he still felt like he was going throw up or pass out. He did miss Earth and seeing the large blue and green planet made him feel homesick for the first time in three years. “Hey listen whatever happens I’m still here for you,” Quill said giving his mate’s hand a firm squeeze.   
“I know, it‘s just...what if things are worst down there? I mean Spiderman is part of me but it’s now just a bad memory.”   
“Sweetheart I’ve seen you fight and you are at your happiest when you’re kicking some bad guy ass, Spiderman isn’t a bad memory it just bad memories follow people like us.” 

He leans over and kisses him on the lips before resting his forehead against the omega’s forehead. He could still smell Peter anxiety he swears he could almost taste it, he moves and curls his hand into Peter’s chocolate soft curls making the omega shudder and sight. “Stark didn’t sound mad when you talked to him.” It was hard to say Peter spent much of them crying, his hormones hitting hard at that moment in time; all Stark could do was try and calm him down as Quill tried his best from his end.  
“He will when he sees Star-Lord Baby bump.” Peter points to his stomach, he was only 5 months long and the bump looked small but still easily spotted.  
“Star Spider.” Peter laughed as the alpha pressed his hand to the bump.   
“Yeah Star Spider.”

Tony paced as he watched the ship hand he tried not to rub his hands together over and over, he needs to show Peter he was still strong and he also needs to show Quill that he is a dead man. Pepper stood by his side she smiled at him and she rubbed his shoulder. “Don’t get mad at him, he was scared and confused when he ran away and getting over a broken bond.”   
“I know, but I snap first and then realise I was an idiot and pretend I didn’t do anything while trying to fix it.” She hmms at him and pats his back.   
“Yes, that is why I’m your better half.” He looks at her as she smiles “Try and not be an idiot, you can yell at Quill.”   
“Yell at him? No, I’m going to kill him.” Pepper shook her head just as they watched two people walk towards them. 

Tony stared as he watched Peter walk towards him, he was different taller but still slim has that butter wouldn’t melt look on his face, his hair was longer more of a mess of curls that reminded him of Harley when he was a kid. His clothes were different something he must have picked up on his travels with Quill, they hugged his body in all the right places Tony thought…bad Tony, stop thinking of your pup like that…he thought to himself. Quill curved his arm around Peter’s waist that that had Tony riled up …what the fuck does he think he is doing that little Shit Lord!… then he saw it the bump the change in Peter’s figure when the omega place hand over it to soothe the rolling pup within him. “H-Hi!” Peter said he stood almost eye level with Tony and the older man looked at Peter’s face things were different but the same.

He reaches out and pulls him for a hug “Oh god kid.” He whispers as he buries his face into Peter’s shoulder. He could smell Quill the alpha was all over Peter almost embedded into his scent; the problem was it complemented the omega’s natural scent and it wasn’t off-putting. Peter hugged back and sobbed into Tony’s shoulder.   
“I’m sorry for running away, I’m sorry for everything...” Tony was expecting his reaction from the kid as he warped his arms around Peter as he did after Bruce back them all back from the land of dust.   
“You got nothing to be sorry for.” He then whispered, “I will, however, have to kill your alpha.” Peter let out a weak chuckle. It was Pepper who slapped the other alpha cross the face before laying into him.


	5. Chapter 5

Quill rubbed his jaw as he looked in the mirror, he could feel could see a bruise forming on his cheek where Pepper had hit him…man that woman packs a punch…he thinks to himself as he sees Peter through the mirror watching him from the bed “I’m sorry she hit you.” Peter tells him. Quill just chuckles as he sees the puppy eyes his mate his giving him as he turns to the bed.   
“Its fine petty boy no harm done.” He smiles he walks over to the bed and cups his face. “How are you feeling?” He asked seeing that the omega’s eyes were still red and puffy.   
“I’m okay.” He tells him   
“Really? You don’t sound so sure?” Peter shrugged and looked down onto the bed. 

Frowning Quill sits next to him and took his hand into his hand “Are you thinking about him?” He asked Peter looked up his eyes widen before he nodded and whimpered as he tilted his head at him offering up his throat.  
“I’m sorry alpha.” He whispered, growling softly the alpha leaned in and kissed Peter’s throat feeling him shiver and whimper as he was pulled onto his lap.   
“You have nothing to be sorry for.” Quill rumbled as he mouthed the young omega’s throat as he lets his hand grip his hips overlapping on the bruises he left behind from earlier. “He was a monster Peter, he took advantage of a vulnerable boy who was still morning the loss of his father figure and dealing with the fact that he had died and been dead for 5 years.” Peter looked back at him as Quill tucked a bit of his hair behind his ears and kissed him on the lips drawing a purr out of his omega. “And his cruellest act he pulled was not the videos he leaked Peter, it was him telling you that he cared for you even after he had been found out and he wanted to corrupt you. He was a cruel sick man.” The omega sniffed and pressed his head onto the alpha’s shoulders “I’m only sorry that I didn’t kill the dick head myself.”   
“Well, that is you and me both porcupine.” Came the voice hind them. 

Peter jumped and looked right up at the other alpha in the room and blinked in shock as Quill turned to frown at Tony. “Hey ever heard of knocking?” Star-Lord asked   
“Have you ever heard of letting us fucking know where my pup is to my wife?” He growls back at him, he had his arms across over his chest as Quill curled his arms around his pregnant mate.   
“I-I wouldn’t let him tell her,” Peter said, Tony frowned and walked more to the room, Peter detangled himself from his alpha that caused Quill to groan at the loss of his omega.   
“I’m going to go for a shower, I will let you two talks and then me and alpha Daddy here will talk.” He kisses Peter on the top of his head and then walks to the bathroom. Peter watches Quill grin at the shower and shook his head, his alpha loved Earth showers the ones on the ship is a little weak.   
“Hey come on let’s go and get something to eat my treat I will buy, what are you fancying?” Tony said as Peter looks at him and then out the window, it’s been a while since Peter been on Earth and going out there to the world that shuns him scared him. “It will be fine.” He smiled  
“Okay.” 

Tony took him to a pizza place where he watched the omega eat about 3 large pizzas to himself filled with everything, he guessed it was the cravings and said nothing of it “How does it feel to be back?” Peter asked him with his cheeks puffed out with pizza.   
“Truthfully? I feel like I’ve been falling through space in a million, billion pieces and then been thrown back together and squished into one tiny pace.” He says, he looks up from his coffee to see Peter looking at him with a concerned frown “But otherwise I’m good.” He tells him “But hey the best part is all my old wounds seem to be gone, no scars no old healed broken bones and I feel like I’m a hundred younger.”  
“I feel confused,” Peter mumbled as he took a sip from his cola.   
“Yeah you and me both.”

He was aware that people were looking at them maybe it was because Tony Stark was sat there maybe it was because someone recognised him, or maybe it was the fact he was dressed like he was going to an SCI-FI convention. Either way, he tried to ignore the looks and turned to look back at Tony who finely spoke again after going quiet for a long time. He watches as the young man reaches out for his ice cream Sunday before asking him. “Gona tell me about what happen between you a Beck?” He asked Peter licked the spoon before he spoke.   
“He was charming, handsome and good in bed, his scent seemed truthful even Nick Fury believed he was a good guy. He fucked me and fucked me up and then destroyed me. Want to know more?” Peter turned to him and tilted his head.   
“Yes but maybe for another day, let’s talk about you and the Arthur Dent wannabe.”   
“Who is Arthur Dent?”

**Author's Note:**

> other chapters may follow


End file.
